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Bug 1203 - memory leak with python script
memory leak with python script
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-12-08 13:04 CST by Aryeh Weiss
Modified: 2015-12-19 10:24 CST
4 users (show)

See Also:
Description Aryeh Weiss 2015-12-08 13:04:49 CST 
This is a continuation of a thread going on in the mailing list.
The problem appears to involve memory allocated to images not being freed in after the script is completed. 
Here is a minimal script that shows some aspects of this:
from ij import IJ, Prefs, ImagePlus
from ij.io import DirectoryChooser,  OpenDialog
from ij.process import ImageConverter, ByteProcessor, BinaryProcessor

op = OpenDialog("Choose input image...", "")
path = op.getDirectory()+ op.getFileName()
inputName = op.getFileName()
inputDir = op.getDirectory()
inputPath = inputDir + inputName

if inputName[-4] == ".":
    inputPrefix = inputName[:-4]    # assumes that a suffix exists
else:
    inputPrefix = inputName


inputImp = ImagePlus(inputPath)
inputImp.show()
ImageConverter(inputImp).convertToGray8()

# The following line makes all the difference.
# inputIp = inputImp.getProcessor()

The line
inputIp = inputImp.getProcessor()

makes a reproducible difference. If it exists, then after running this program, the image memory is not freed.
If I run this script multiple times, it seems to retain one copy (maybe it overwrites the reference).

If I comment out this line, then gc will free all of the memory.
Moreover, if I ran it with this line uncommented, and the memory got "stuck", and then I run it without
this line (ie commented out), the next gc will free *all* of the memory.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.11.1
  java.version => 1.8.0_66
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_66-b17
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.66-b17
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/local/fiji/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20151122035629)
Fiji: http://update.fiji.sc/ (last check:20151207132153)
3D: http://sites.imagej.net/3D/ (last check:20151124051031)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20151207101225)
BAR: http://sites.imagej.net/Tiago/ (last check:20150923213109)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20151205042647)
Biomedgroup: http://sites.imagej.net/Biomedgroup/ (last check:20151201102656)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20151207234930)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20150303000629)
CMCI-EMBL: http://sites.imagej.net/Miura/ (last check:20151013151911)
GDSC: http://sites.imagej.net/GDSC/ (last check:20151204124542)
GDSC-SMLM: http://sites.imagej.net/GDSC-SMLM/ (last check:20151020151423)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20150318120643)
IJPB-plugins: http://sites.imagej.net/IJPB-plugins/ (last check:20151127183509)
LOCI: http://sites.imagej.net/LOCI/ (last check:20150429005912)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723175558)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20151119200830)
PTBIOP: http://biop.epfl.ch/Fiji-Update/ (last check:20151204162832)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20150820182346)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20141221170506)

Files not up-to-date:
  99b483f6 (MODIFIED) 20151206222513 Contents/Info.plist
  c6691924 (MODIFIED) 20151207130510 jars/ij-1.49v.jar
  1ad3be0d (LOCAL_ONLY) 20140611011244 jars/jpedalSTD.jar
  d79f9ea6 (LOCAL_ONLY) 20131229114506 luts/ND1-6-11-23 despecal.lut
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  e78a6849 (LOCAL_ONLY) 20140916101545 macros/AutoRun/testInstall.ijm
  2f19e4ec (LOCAL_ONLY) 20110616115254 macros/BatchMacro.ijm
  7ac59f8a (LOCAL_ONLY) 20110205211055 macros/Mark_objects.ijm
  2bed7e59 (LOCAL_ONLY) 20110205211252 macros/Mark_patterns.ijm
  c630043e (LOCAL_ONLY) 20111116203833 macros/OpenFileList.txt
  5f405e9f (LOCAL_ONLY) 20100118100436 macros/PSA_dev.txt
  d4f8abbe (LOCAL_ONLY) 20100118100420 macros/PSA_r12.txt
  e991a157 (LOCAL_ONLY) 20140703155151 macros/Particle_Classifier.ijm
  abb807be (LOCAL_ONLY) 20130623143925 macros/Particle_Classifier.txt
  545e8639 (LOCAL_ONLY) 20140828052548 macros/RunAtStartup.ijm
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  cb3df91c (LOCAL_ONLY) 20130319071610 macros/cicleGrid.ijm
  6f74d729 (LOCAL_ONLY) 20110822153016 macros/claheStack.ijm
  6f901fd0 (LOCAL_ONLY) 20120418131404 macros/corr_bleach050405.txt
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  a71f6a6b (LOCAL_ONLY) 20140512132921 macros/deleteROIa.ijm
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  d62aa133 (LOCAL_ONLY) 20090816231515 macros/focus_macro_2.txt
  43a15391 (LOCAL_ONLY) 20140510222831 macros/gridTool.ijm
  88d4bd3e (LOCAL_ONLY) 20080127212656 macros/henis-1a.txt
  32108318 (LOCAL_ONLY) 20120124171147 macros/landini_startup.ijm
  b6eda886 (LOCAL_ONLY) 20080917110344 macros/naomi_fix_filenumbers.txt
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  28276e43 (LOCAL_ONLY) 20090914120859 macros/nrg010.txt
  bcf0803e (LOCAL_ONLY) 20090914113101 macros/nrg010_amw.txt
  bc690cb9 (LOCAL_ONLY) 20091015102920 macros/nrg016_amw.txt
  8aa156f2 (LOCAL_ONLY) 20091028095405 macros/nrg022.txt
  10c27176 (LOCAL_ONLY) 20130319071527 macros/randomLines.ijm
  a4351c75 (LOCAL_ONLY) 20130419085326 macros/recursiveDirSearch.ijm
  63598ced (LOCAL_ONLY) 20100720141138 macros/red_to_magenta.txt
  30324b71 (LOCAL_ONLY) 20110818141531 macros/resizeROIs.ijm
  1a4001e2 (LOCAL_ONLY) 20090927105412 macros/time_stamp.txt
  3da9830a (LOCAL_ONLY) 20130301160716 macros/toolsets/MiToBo_Runner.txt
  4794b9ba (LOCAL_ONLY) 20131216070147 macros/toolsets/ROI Manager Tools.txt
  9a9b8420 (LOCAL_ONLY) 20140209141104 mmautofocus/MMAutofocus.jar
  8a993e35 (LOCAL_ONLY) 20131207201338 mmautofocus/MMAutofocusDuo.jar
  0524fa64 (LOCAL_ONLY) 20140209141104 mmautofocus/MMAutofocusTB.jar
  ef6fd981 (LOCAL_ONLY) 20140209141104 mmautofocus/MMOughtaFocus.jar
  e02925cd (LOCAL_ONLY) 20140209141100 mmplugins/SPIMAcquisition.jar
  fc81f390 (LOCAL_ONLY) 20150828232520 plugins/2015 Conference/01_Sphere_Macro.ijm
  55b39591 (LOCAL_ONLY) 20150828152300 plugins/2015 Conference/02_Sphere_JavaScript.js
  25fd3aa3 (LOCAL_ONLY) 20150828152946 plugins/2015 Conference/03_Sphere_BeanShell.bsh
  59f964d3 (LOCAL_ONLY) 20150828153034 plugins/2015 Conference/04_Sphere_Python.py
  a7c7e535 (LOCAL_ONLY) 20150901234226 plugins/2015 Conference/06_Plot_Features.ijm
  4f04d824 (LOCAL_ONLY) 20150827233840 plugins/2015 Conference/07_Example_Plot.ijm
  d21311fd (LOCAL_ONLY) 20150827234608 plugins/2015 Conference/08_Arrow_Plot.ijm
  2ad7a2f2 (LOCAL_ONLY) 20150827235254 plugins/2015 Conference/09_Semi-log_Plot.ijm
  d7ff26c4 (LOCAL_ONLY) 20150901231746 plugins/2015 Conference/10_Error_Bars.ijm
  81ae2453 (LOCAL_ONLY) 20150831214012 plugins/2015 Conference/11_Grab_Viridis_Colormap_.ijm
  cdff63e8 (LOCAL_ONLY) 20150828002928 plugins/2015 Conference/12_Display_LUTs_.ijm
  d6fb52d2 (LOCAL_ONLY) 20150828003520 plugins/2015 Conference/13_Startup_.ijm
  ea1ab9a4 (LOCAL_ONLY) 20150830103406 plugins/2015 Conference/14_Reset_Preferences.ijm
  67c1be34 (LOCAL_ONLY) 20150828001214 plugins/2015 Conference/15_Non-numeric_Table_.ijm
  00a160f0 (LOCAL_ONLY) 20150901224442 plugins/2015 Conference/16_Dialog_with_Image_and_Help.js
  24f463a2 (LOCAL_ONLY) 20150901233416 plugins/2015 Conference/17_Radio_Buttons.js
  7136cf0b (LOCAL_ONLY) 20150901230916 plugins/2015 Conference/18_Set_Spline_Anchors.ijm
  7c9c2784 (LOCAL_ONLY) 20150828151634 plugins/2015 Conference/19_Dual_Progress_Bars_.js
  48f6c4f2 (LOCAL_ONLY) 20150828162140 plugins/2015 Conference/20_Point_Selections.ijm
  d685c315 (LOCAL_ONLY) 20150901222422 plugins/2015 Conference/21_HeLa_Cells.ijm
  e52c825a (LOCAL_ONLY) 20150901220906 plugins/2015 Conference/22_Arrange_Channels.js
  526e7cbe (LOCAL_ONLY) 20150902001558 plugins/2015 Conference/23_Gamma_Adjuster.js
  da32e2be (LOCAL_ONLY) 20150827232420 plugins/2015 Conference/24_Lab Colorspace.ijm
  59b0eb01 (LOCAL_ONLY) 20150901233200 plugins/2015 Conference/25_Overlay_Translation.js
  7afb5a0b (LOCAL_ONLY) 20150828002322 plugins/2015 Conference/26_Rotated_Text_.js
  8d509e80 (LOCAL_ONLY) 20150829002846 plugins/2015 Conference/Sphere_Plugin.class
  81368c3d (LOCAL_ONLY) 20090520001428 plugins/3D/3d-oc_.jar
  dd0089ce (LOCAL_ONLY) 20090519115018 plugins/3D/Object_Counter3D.class
  5a02e888 (LOCAL_ONLY) 20120717140527 plugins/3D/VoltIJ_.jar
  d75ceaf3 (LOCAL_ONLY) 20090723113800 plugins/3D/WatershedCounting3D_Instructions.txt
  81f10d1d (LOCAL_ONLY) 20090723113752 plugins/3D/WatershedCounting_3D.jar
  2d117ad9 (LOCAL_ONLY) 20100701083659 plugins/AccPbFRET_Plugin.class
  af1bd32b (LOCAL_ONLY) 20100701083659 plugins/AcceptorCTCorrDialog.class
  51cf8d93 (LOCAL_ONLY) 20100701083659 plugins/AcceptorPPCorrDialog.class
  42d1a127 (LOCAL_ONLY) 20130604183909 plugins/ActionBar/Shared Bars/BIOP_HRM_Manager.ijm
  bd7bc5d1 (LOCAL_ONLY) 20140605154244 plugins/ActionBar/Shared Bars/BIOP_MultiManualSelect.ijm
  c271b415 (LOCAL_ONLY) 20140605154244 plugins/ActionBar/Shared Bars/BIOP_PSF_Quality.ijm
  e9bf0b0f (LOCAL_ONLY) 20130625065921 plugins/ActionBar/Shared Bars/BIOP_SIMAssess.ijm
  08afb731 20140310145147 plugins/ActionBar/Shared Bars/BIOP_VSI_Reader.ijm
  b27361cb (LOCAL_ONLY) 20151021142709 plugins/ActionBar/Shared Bars/BIOP_VSI_reader.ijm
  4edb1d6f (LOCAL_ONLY) 20140605154245 plugins/ActionBar/Shared Bars/Common_Tools.ijm
  db280c9c (LOCAL_ONLY) 20140315231112 plugins/ActionBar/Shared Bars/JaCoP_Tools.ijm
  fc766719 (LOCAL_ONLY) 20090805063824 plugins/Adrian_FWHM.jar
  2076fd3d (LOCAL_ONLY) 20110509181247 plugins/Analyze/Auto_Corr.class
  0faf81bc (LOCAL_ONLY) 20110509181134 plugins/Analyze/Auto_Corr_AW.class
  b7c33b97 (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$1.class
  ed0770b8 (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$2.class
  df5364aa (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$3.class
  649faa7f (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$4.class
  ad4ad3b7 (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$5.class
  e5892834 (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$6.class
  ea85a145 (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$7.class
  64fb05a7 (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$8.class
  2f965736 (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$SliceMover.class
  28b7646e (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner$SliceSetter.class
  798d5b01 (LOCAL_ONLY) 20091223092558 plugins/Analyze/Cell_Outliner.class
  07f433a4 (LOCAL_ONLY) 20091209125709 plugins/Analyze/Hough_Circles.class
  757c47ea (LOCAL_ONLY) 20110202121422 plugins/Analyze/IntraCell_v1.class
  265de9a4 (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$1.class
  052c8fa8 (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$2.class
  0f0f3ebf (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$3.class
  d174ffd1 (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$4.class
  05b04d7f (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$5.class
  8e8c9c1f (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$6.class
  d70f7c92 (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$7.class
  91d9e8b3 (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$8.class
  a1baffb2 (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$SliceMover.class
  1a5b7df4 (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$SliceSetter.class
  7da88be3 (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner$WandMM.class
  66ebe0b3 (LOCAL_ONLY) 20091125100519 plugins/Analyze/Multi_Cell_Outliner.class
  435937fb (LOCAL_ONLY) 20130818071157 plugins/Analyze/Nnd_.class
  ebeb645f (LOCAL_ONLY) 20091223092558 plugins/Analyze/WandMM.class
  f9f617b5 (LOCAL_ONLY) 20131104101336 plugins/Analyze/analyze_stripes_v2.4.1.ijm
  b41e0913 (LOCAL_ONLY) 20110429164014 plugins/Analyze/stack_counter.jar
  287c3f2c (LOCAL_ONLY) 20100822230259 plugins/AnalyzeSkeleton$1.class
  4dd99988 (LOCAL_ONLY) 20100822230259 plugins/AnalyzeSkeleton.class
  69d17271 (LOCAL_ONLY) 20100701083659 plugins/ApplyMaskDialog.class
  324f928d (LOCAL_ONLY) 20111031095200 plugins/Auto_Align_1.jar
  3e08906a (LOCAL_ONLY) 20150924145414 plugins/BIOP/BIOP_VSI_reader/BIOP_VSI_reader.ijm
  82418c28 (LOCAL_ONLY) 20130529090002 plugins/BioVoxxel_Toolbox.ijm
  606743ae (LOCAL_ONLY) 20130824225122 plugins/Blend_Images.class
  7f6d6194 (LOCAL_ONLY) 20120225185825 plugins/Blob_Prob.jar
  59a303cc (LOCAL_ONLY) 20120429112745 plugins/BoneJ_.jar
  ab8a8b5e (LOCAL_ONLY) 20150722020718 plugins/CANDLE-J/CANDLE.py
  8a316fa7 (LOCAL_ONLY) 20150722022008 plugins/CANDLE-J/InverseAnscombe.class
  c2c8d4e0 (LOCAL_ONLY) 20150722022420 plugins/CANDLE-J/NativeCodeJNA$NoiseEstimationInterface.class
  37d725ed (LOCAL_ONLY) 20150722022420 plugins/CANDLE-J/NativeCodeJNA$ONLMInterface.class
  d4b76cf3 (LOCAL_ONLY) 20150722022420 plugins/CANDLE-J/NativeCodeJNA.class
  56b568bf (LOCAL_ONLY) 20141119063824 plugins/CANDLE-J/jna-4.1.0.jar
  7a8c0c47 (LOCAL_ONLY) 20141119063828 plugins/CANDLE-J/jna-platform-4.1.0.jar
  6ddd37a8 (LOCAL_ONLY) 20130328044546 plugins/CUDA_Deconvolution.jar
  7eee9a1d (LOCAL_ONLY) 20100701083659 plugins/CalculateImgRatioDialog.class
  65ab9874 (LOCAL_ONLY) 20100512073356 plugins/Colony_Counter.jar
  bfdf66c3 (LOCAL_ONLY) 20100714203838 plugins/Colour functions/Align_RGB_planes.class
  4da741fc (LOCAL_ONLY) 20120724065825 plugins/Colour functions/ColorSegmentation_.jar
  0a5c1981 (LOCAL_ONLY) 20080220153008 plugins/Colour functions/Color_Profiler.jar
  63cef19d (LOCAL_ONLY) 20121105191335 plugins/Colour functions/Color_Space_Converter$ColorSpaceConverter.class
  933620c3 (LOCAL_ONLY) 20121105191335 plugins/Colour functions/Color_Space_Converter.class
  ed9a6168 (LOCAL_ONLY) 20070416171000 plugins/Colour functions/Colour_Balance.class
  05883551 (LOCAL_ONLY) 20050512174136 plugins/Colour functions/Colour_Correct.class
  365af84e (LOCAL_ONLY) 20050201173722 plugins/Colour functions/Colour_merge.class
  4a5615b5 (LOCAL_ONLY) 20070626205056 plugins/Colour functions/HSV_Stack.class
  d24cd2d1 (LOCAL_ONLY) 20070626205118 plugins/Colour functions/Lab_Stack.class
  199930f3 (LOCAL_ONLY) 20070626205128 plugins/Colour functions/Luv_Stack.class
  af44f592 (LOCAL_ONLY) 20070620105212 plugins/Colour functions/RGB_Gray_Merge.class
  e9928b83 (LOCAL_ONLY) 20050512170626 plugins/Colour functions/RGB_Measure.class
  ed01e3ec (LOCAL_ONLY) 20130419090306 plugins/Colour functions/RGB_Measure_Plus.class
  7cf305a0 (LOCAL_ONLY) 20040408181504 plugins/Colour functions/RGB_Profiler.class
  f26d321b (LOCAL_ONLY) 20050106165130 plugins/Colour functions/RGB_recolor .txt
  12af1bda (LOCAL_ONLY) 20070214143600 plugins/Colour functions/RGB_to_Montage.class
  6ad1190e (LOCAL_ONLY) 20061011151400 plugins/Colour functions/Recolor_RGB_to_MGB.txt
  67914d0c (LOCAL_ONLY) 20050527180332 plugins/Colour functions/Resize2Rotate_.txt
  109660fc (LOCAL_ONLY) 20100708165138 plugins/Colour functions/Retinex_.class
  5b673829 (LOCAL_ONLY) 20110529055137 plugins/Colour functions/SmartCapture_Lite.jar
  3273d22c (LOCAL_ONLY) 20070126123500 plugins/Colour functions/Whiten_background.class
  f0854dbd (LOCAL_ONLY) 20130319115246 plugins/Common_Toolbar_amw.class
  52ff6766 (LOCAL_ONLY) 20100211190655 plugins/Create_Template.jar
  8d9bdfa0 (LOCAL_ONLY) 20090703152912 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  d14a7cbc (LOCAL_ONLY) 20090625171804 plugins/Depth_from_focus.class
  6a87ed7d (LOCAL_ONLY) 20100701083659 plugins/DonorBlCorrDialog.class
  44c67a2f (LOCAL_ONLY) 20151103120934 plugins/Droplet Actions/Open as 8-bit.ijm
  dec56900 (LOCAL_ONLY) 20081202161412 plugins/EDF/Demo.class
  52b4532b (LOCAL_ONLY) 20081202161546 plugins/EDF/EDF-demo.txt
  fc7d947e (LOCAL_ONLY) 20081202161412 plugins/EDF/EDF_Easy_$1.class
  460c8107 (LOCAL_ONLY) 20081202161412 plugins/EDF/EDF_Easy_.class
  b87549d6 (LOCAL_ONLY) 20081202161412 plugins/EDF/EDF_Expert_$1.class
  eecd3775 (LOCAL_ONLY) 20081202161412 plugins/EDF/EDF_Expert_.class
  bb4d8598 (LOCAL_ONLY) 20081202161412 plugins/EDF/EDF_Viewer3D_$MainDialog.class
  1f8adba2 (LOCAL_ONLY) 20081202161412 plugins/EDF/EDF_Viewer3D_.class
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  ef475177 (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/EdfRealWavelets.class
  7510215e (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/EdfSobel.class
  c5aae14a (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/EdfVariance.class
  65434783 (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/EdfWaveletMaximumModulus.class
  2f0e80f0 (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/LogSingleton.class
  0ffe4e0d (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/MorphologicalOperators.class
  f434f107 (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/PostProcessing.class
  9441e9e6 (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/ProcessTopology.class
  0187d9a9 (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/Sobel.class
  c653047b (LOCAL_ONLY) 20081202161412 plugins/EDF/edf/Tools.class
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  56f0b03f (LOCAL_ONLY) 20081202161412 plugins/EDF/edfgui/AboutDialog.class
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  794d8ccb (LOCAL_ONLY) 20081202161412 plugins/EDF/edfgui/AbstractDialog.class
  cdb53d41 (LOCAL_ONLY) 20081202161412 plugins/EDF/edfgui/AdvancedDialog$MyVerifier.class
  0fdfdf3d (LOCAL_ONLY) 20081202161412 plugins/EDF/edfgui/AdvancedDialog.class
  5bed4a73 (LOCAL_ONLY) 20081202161412 plugins/EDF/edfgui/BasicDialog.class
  dcb35ca5 (LOCAL_ONLY) 20081202161412 plugins/EDF/edfgui/ExtendedDepthOfField.class
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  2a3ab5f0 (LOCAL_ONLY) 20081202161412 plugins/EDF/edfgui/MySlider.class
  ad85c9b5 (LOCAL_ONLY) 20081202161412 plugins/EDF/edfgui/MyTableRenderer.class
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  fc5d4c0d (LOCAL_ONLY) 20081202161412 plugins/EDF/edfgui/ThreadTopoProc.class
  b77b5da8 (LOCAL_ONLY) 20081202161412 plugins/EDF/imageware/Access.class
  895118eb (LOCAL_ONLY) 20081202161412 plugins/EDF/imageware/Buffer.class
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  b6bf3817 (LOCAL_ONLY) 20070308105404 plugins/local/edu_mines_jtk.jar
  64530315 (LOCAL_ONLY) 20120113054956 plugins/local/flyover.js
  cc688631 (LOCAL_ONLY) 20111109144712 plugins/metroloj_.jar
  6990c9bc (LOCAL_ONLY) 20100426225303 plugins/objectj_.jar
  2d053fcd (LOCAL_ONLY) 20110812150426 plugins/qr_decoder_1.0.jar
  c1b00ab5 (LOCAL_ONLY) 20110130100511 plugins/sfcm_clustering.jar
  09dec5ec (LOCAL_ONLY) 20140307131816 plugins/slim_plugin-2.0.0-SNAPSHOT.jar
  32546563 (LOCAL_ONLY) 20110320213938 plugins/tracer/Bare_PlugInFilter1.class
  d0c3d14c (LOCAL_ONLY) 20110318131006 plugins/tracer/RunIt.class
  bbc2eaff (LOCAL_ONLY) 20110320203538 plugins/tracer/fixer.class
  5d99cb0b (LOCAL_ONLY) 20140318112640 scripts/find_peaks.bsh
  41af04e2 (LOCAL_ONLY) 20131028202729 scripts/very_basic_camera_test.bsh
Comment 1 Mark Hiner 2015-12-08 15:05:13 CST 
Looking at your files, I noticed you have a file:

"plugins/jars/Jython.jar"

that looks suspicious to me. We ship a copy of Jython - it should be located in:

"jars/jython-shaded-2.5.3.jar"

Would you mind doing two things and testing again:
1) make sure you have the jython-shaded.jar, and 
2) move the plugins/jars/Jython.jar out of your Fiji installation, at least temporarily for testing purposes.

I am hoping that the plugins/jars/Jython.jar is an older version of Jython that has known memory problems...
Comment 2 Wayne Rasband 2015-12-08 16:52:26 CST 
I am unable to reproduce this problem using a 1GB, 16-bit tiff stack (1024x1024x512), on either ImageJ or Fiji. Using the Memory Monitor, I see that memory usage peaks at 1300MB, drops to 544MB when I click a few times in the "Memory" window, and then drops to 32MB after I close the stack and click a few more times. There is a relatively small (~25MB) memory leak probably caused by memory used by Jython not being reclaimed.
Comment 3 Aryeh Weiss 2015-12-08 23:08:59 CST 
Concerning the python.jar:
This was added whenI needed to evaluate a python script from a plugin - 
    eval("python", script);
When I did this, it prompted me that I to install Jython.jar, and it even was kind enough to do it for me.

Motivated by Mark's comment, I renamed that jython to python.old, and copied the Jython snapshot file (which was in jars) to the plugin/jars directory (and renamed that one to jython.jar). The results are the same for my minimal script

I modified my minimal script to run the gc, and then close the image and runthe gc again (twice). 

So here is the new script:
from ij import IJ, Prefs, ImagePlus
from ij.io import DirectoryChooser,  OpenDialog
from ij.process import ImageConverter, ByteProcessor, BinaryProcessor
import time, gc

def forceGc():
	print "memory before gc = ", IJ.currentMemory()
	gc.collect()
	print "memory after gc = ", IJ.currentMemory()


op = OpenDialog("Choose input image...", "")
path = op.getDirectory()+ op.getFileName()
inputName = op.getFileName()
inputDir = op.getDirectory()
inputPath = inputDir + inputName

if inputName[-4] == ".":
    inputPrefix = inputName[:-4]    # assumes that a suffix exists
else:
    inputPrefix = inputName


inputImp = ImagePlus(inputPath)
inputImp.show()
ImageConverter(inputImp).convertToGray8()

# The following line makes all the difference.
inputIp = inputImp.getProcessor()
forceGc()

inputImp.close()
forceGc()
forceGc()


and here is the output with an image of about 1 GB:

Started minimal.py at Wed Dec 09 07:06:54 IST 2015
memory before gc =  1037433016L
memory after gc =  1042983208L
memory before gc =  1058432336L
memory after gc =  1044836632L
memory before gc =  1044836632L
memory after gc =  1041655776L

## end offers run on "fresh" Fiji 

Started minimal.py at Wed Dec 09 07:07:12 IST 2015
memory before gc =  2055344376L
memory after gc =  1044025032L
memory before gc =  1056477256L
memory after gc =  1042805472L
memory before gc =  1042971816L
memory after gc =  1036835368L

## end of second run -- nothing open

Wayne -- can you run this script and post the result?
Comment 4 Wayne Rasband 2015-12-08 23:31:46 CST 
This is the output I get when I run the new test script using a 1GB stack:

Started Untitled.ijm.py at Wed Dec 09 00:17:41 EST 2015
memory before gc =  912628040L
memory after gc =  573682104L
memory before gc =  573963312L
memory after gc =  37250824L
memory before gc =  37252912L
memory after gc =  37228416L
Comment 5 Aryeh Weiss 2015-12-09 01:26:11 CST 
There is something about getProcessor()
In my script I had two getProcessor() calls which I could remove

resultDupIp = resultDupImp.getProcessor() # (at about line 250)
and 
maskIp = maskImp.getProcessor()  # (at about line 313)

Removing these called reduced the amount of "stuck" memory from
5.8GB to about 2.9GB

I have two there places that I use the Ip

inputIp = inputImp.getProcessor()
inputImp.setTitle(inputPrefix+"_mono")
monoTitle = inputImp.getTitle()

rf = RankFilters()
rf.rank(inputIp, 1, RankFilters.MEDIAN)


I tried replacing this with: 
IJ.run(inputImp, "Median...", "radius=1");
or even 
IJ.run(inputImp, "Mean...", "radius=1"); 

but this did not change anything. Apparently, the call using the static
method also gets an Ip.

Same thing with:

bgIp = bgImp.getProcessor()
radius = 100.0
accuracy = 0.01
GaussianBlur().blurGaussian( bgIp, radius, radius, accuracy)

which I tried to replace with either
IJ.run(bgImp, "Gaussian Blur...", "sigma="+str(radius));

or 

IJ.run(bgImp, "Mean...", "radius="+str(radius));   # really slow...


but again, no change.

So getProcessor() apparently creates this hard reference...
Comment 6 Aryeh Weiss 2015-12-09 02:00:04 CST 
Here is something that may be related.
I tried to create a small java plugin to open an image, run the Gaussian blur, and then close it, to see what happens with the memory. However, when I tried to run it, I got the following error:

Started My_Plugin.java at Wed Dec 09 09:54:38 IST 2015
Compiling 1 file in /var/folders/z5/zp1ywtqs03q4g1jltsnm7bbr0000gs/T/java2155939277511209585
/var/folders/z5/zp1ywtqs03q4g1jltsnm7bbr0000gs/T/java2155939277511209585/src/main/java/My_Plugin.java:7: cannot access java.lang.Object
bad class file: ZipFileIndexFileObject[/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Object.class)]
class file has wrong version 52.0, should be 50.0
Please remove or make sure it appears in the correct subdirectory of the classpath.
public class My_Plugin implements PlugIn {
       ^
org.scijava.minimaven.JavaCompiler$CompileError: Compile error: 1
	at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:80)
	at org.scijava.minimaven.MavenProject.build(MavenProject.java:477)
	at org.scijava.minimaven.MavenProject.build(MavenProject.java:406)
	at org.scijava.minimaven.MavenProject.build(MavenProject.java:391)
	at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:211)
	at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)
	at ...
+more stuff I will add if relevant.

Is my java configured incorrectly?
Comment 7 Wayne Rasband 2015-12-09 22:01:46 CST 
I cannot reproduce this problem. I suspect there is something wrong with your Fiji installation. You could try downloading a fresh copy of Fiji and running the test script on it. Or try running the test script on another computer.
Comment 8 Aryeh Weiss 2015-12-10 01:04:30 CST 
I downloaded a fresh Fiji, and ran my minimal script in it.
The results were the same.
I deselected all of the update sites except ImageJ and Fiji, and still
have the same result.
One thing -- I am loading a single image that is about 1Gpixel.
If you are loading a stack, maybe the memory allocation is done differently?

I will upload a heapstack with the fresh Fiji, and also an example image, when I am next at a high speed connection.
Comment 9 Aryeh Weiss 2015-12-10 02:45:32 CST 
I tried my minimal script on a Win7-64bit machine, and found the same result.
Here is a link to my test-image:
https://www.dropbox.com/s/a0qsgc2kei89ssq/testImage.zip?dl=0

I uploaded a heap dump with the Fiji upload-sample-image command.
Comment 10 Wayne Rasband 2015-12-10 09:18:50 CST 
I can reproduce the problem using a 1GB 16-bit image (23170x23170) and the following minimal Python script. Jython appears to be holding a reference to 'ip' after the script ends. Adding "ip=None" to the script does not help. One workaround is to use JavaScript.

IJ.doCommand("Monitor Memory...")
img=IJ.openImage("")
ip=img.getProcessor()
img.close()
Comment 11 Curtis Rueden 2015-12-10 09:38:44 CST 
I am curious whether this bug in Jython has been fixed with version 2.7.0.

You can try replacing jars/jython-shaded-2.5.3.jar with this one:
   http://curtis.imagej.net/2015-12-10-jython/jython-shaded-2.7.0.jar

But note that this version of Jython requires Java 7 or later.
Comment 12 Aryeh Weiss 2015-12-10 12:54:28 CST 
I just tried it, and used sys.version to verify that I was  running 2.7.0.
The bug is still present.
Comment 13 Mark Hiner 2015-12-14 12:38:03 CST 
It's definitely an issue with our implementation of the jython script language. The python environment is not cleaned up after running a script - and in fact there is code that relies on the environment not being cleaned up.

You can hack it right now and effectively "force" the scope of the variables to be respected, by explicitly setting them to None before your script ends.

e.g.:

   inputIp = inputImp.getProcessor()
   #... do some stuff with the IP...
   inputIp = None

will ensure the image processor doesn't stick around. But that is, of course, terrible.

I've been looking at options for cleaning up the python environment[1] but the timing of when to do so is tricky.

I'll keep trying...


[1] http://python.6.x6.nabble.com/Cleaning-up-PythonInterpreter-object-td1777184.html
Comment 14 Aryeh Weiss 2015-12-14 14:10:12 CST 
adding inputIp=None works with my minimal script.

However, in my full script (which I sent to mark), it does not reduce the "stuck" memory below about 2GB. Here is a snippet:

inputIp = inputImp.getProcessor()
inputImp.setTitle(inputPrefix+"_mono")
monoTitle = inputImp.getTitle()

rf = RankFilters()
rf.rank(inputIp, 1, RankFilters.MEDIAN)

inputIp = None

I get the processor in order to run the RankFilter.

Perhaps something else which I do allocates ImageProcessors, and I cannot free these since I do not have access to them.
Comment 15 Mark Hiner 2015-12-14 15:02:06 CST 
The problem is that EVERY variable you create in the script would have to be manually closed ("None"d out).

Good news though: I have implemented a solution[1] that cleans up the Jython variables after execution. For me it allows memory to be reclaimed after running your test script, WITHOUT explicitly "None"ing the ImageProcessor.

Hopefully we can get this merged and uploaded to Fiji soon.


[1] https://github.com/scijava/scripting-jython/pull/7
Comment 16 Aryeh Weiss 2015-12-15 03:07:45 CST 
How is this used>
Is this a script that I call from my python script? 
Or is it something that needs to be run separately?
Comment 17 Curtis Rueden 2015-12-15 06:43:09 CST 
> How is this used>

It is a bug-fix to the Jython scripting component of ImageJ. The link Mark provided is to a set of patches currently pending review. Once we are sure it the solution is necessary and sufficient, we will merge it into the main codebase.

It is possible to use the bug-fix before that by checking out the branch and building it, but unless your need is extremely urgent I would not advise it. We will try to get it deployed to the ImageJ update site within the next few days.

Once the fix is deployed, the memory problems you are seeing should disappear.
Comment 18 Aryeh Weiss 2015-12-15 09:21:03 CST 
I can wait. Thank you very much.
Comment 19 Mark Hiner 2015-12-18 11:33:37 CST 
If you run Help>Update... to the latest Fiji, this is now fixed.
Comment 20 Aryeh Weiss 2015-12-19 10:24:27 CST 
Appears to work as advertised. Many thanks.